Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 737

System / cell line: type ✕ Clear

Wiggle-predicting functionally flexible regions from primary sequence.

PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

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A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

hiv bovine calmodulin nonredundant gaussian gnm support
MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

PMID 16834459 · PMC1502153 · PLoS medicine · 2006 · 8 claims · 8 setups

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A somatic activating mutation in MPL (W515L, transmembrane domain) is present in 9% (4/45) of JAK2V617F-negative myelofibrosis (MF) patients

granulocyte hapmap 32d balb sequencing genotyping proliferation
Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

genomic same pooled pcr-rflp pcr-based cross-tabulation
A case report of familial benign hypocalciuric hypercalcemia: a mutation in the calcium-sensing receptor gene.

PMID 16642557 · PMC2687637 · Yonsei medical journal · 2006 · 8 claims · 6 setups

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A heterozygous E297K mutation (GAG→AAG, exon 4) of the CaSR gene was identified in a Korean family with FBHH.

genomic proband pcr pcr-rflp bone
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

PMID 16460646 · PMC3525152 · Human genomics · 2006 · 8 claims · 8 setups

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GJB2 (connexin 26) mutations account for hearing loss in only 17 of 156 families (11%), a smaller fraction than reported in other populations.

palestinian genomic probands lymphoblasts targeted sanger pcr
Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

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A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

colorectal cdna matched thyroid rt-pcr restriction genomic
QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

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QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

pubmed ucsc laser-captured literature genome comparative
Proteomics as a tool for biomarker discovery.

PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

serum laser ovarian seldi-tof two-dimensional gene
Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

magi pbmc 293t supt1 sensitive rt-pcr western
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

PMID 17910767 · PMC2148068 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Different CNV analysis software packages produce highly variable numbers and types of candidate CNVs from the same data

normalized individuals subset same affymetrix fluorescent snp
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

PMID 17875208 · PMC2375033 · Genome biology · 2007 · 8 claims · 4 setups

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A subset of C. elegans DAF-19 target genes have Drosophila homologs that are also regulated by dRFX, showing conservation of the RFX regulatory cascade between the two species.

drosophila genome melanogaster real-time comparative gfp
Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

PMID 17849004 · PMC1964532 · PloS one · 2007 · 8 claims · 5 setups

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mtUPR responsive genes (YME1L1, MPPβ, Tim17A, NDUFB2, Endonuclease G, Thioredoxin 2, plus previously known ClpP, Cpn60/10, MtDnaJ) all contain a CHOP element in their promoters

genome cos-7 promoters bioinformatic promoter-luciferase site-directed
Use of functional genomics to understand influenza-host interactions.

PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

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Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

hela a549 lung texas cdna microarray infection
High resolution melting for mutation scanning of TP53 exons 5-8.

PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

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HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

tp53-mutant ovarian breast high hrm dideoxy
Association of Escherichia coli O157:H7 tir polymorphisms with human infection.

PMID 17718910 · PMC2063500 · BMC infectious diseases · 2007 · 8 claims · 6 setups

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tir polymorphisms 255 T>A and RR1-RU3 (presence/absence) associate strongly with human vs bovine isolate source

stec pcr multiplex elisa
Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

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CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

genomic hut78 t-cells direct pcr dual
Fast-evolving noncoding sequences in the human genome.

PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

chimpanzee genome hapmap comparative genomic segmental
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

disease mammalian compiled literature minigene computational

Experiments

Wiggle-predicting functionally flexible regions from primary sequence.

MPLW515L is a novel somatic activating mutation in myelofibrosis with myeloid metaplasia.

Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

A case report of familial benign hypocalciuric hypercalcemia: a mutation in the calcium-sensing receptor gene.

Human SNPs resulting in premature stop codons and protein truncation.

Genomic analysis of a heterogeneous Mendelian phenotype: multiple novel alleles for inherited hearing loss in the Palestinian population.

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

Proteomics as a tool for biomarker discovery.

Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray data.

Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species.

Discovery of genes activated by the mitochondrial unfolded protein response (mtUPR) and cognate promoter elements.

Use of functional genomics to understand influenza-host interactions.

High resolution melting for mutation scanning of TP53 exons 5-8.

Association of Escherichia coli O157:H7 tir polymorphisms with human infection.

Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

Fast-evolving noncoding sequences in the human genome.

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.